I do not have any bad experience. I put my scrivener files in a folder backed up by dropbox and this folder is also backed up by TM. If you worry about TM's behaviour: Just switch it off while working. When you have finished switch it on again
There is no disadvantage of EagleFiler as a »Finder-integrated« solution: You can use EF but you never depend on this software because there is no special data base. For me it's the greatest thing (>30.000 files).